2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>atom_modify command
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</H3>
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<P><B>Syntax:</B>
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</P>
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2010-01-14 04:56:56 +08:00
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<PRE>atom_modify keyword values ...
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2006-09-22 00:22:34 +08:00
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</PRE>
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<UL><LI>one or more keyword/value pairs may be appended
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2010-01-14 04:56:56 +08:00
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<LI>keyword = <I>map</I> or <I>first</I> or <I>sort</I>
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2008-02-16 03:09:18 +08:00
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<PRE> <I>map</I> value = <I>array</I> or <I>hash</I>
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<I>first</I> value = group-ID = group whose atoms will appear first in internal atom lists
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<I>sort</I> values = Nfreq binsize
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Nfreq = sort atoms spatially every this many time steps
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binsize = bin size for spatial sorting (distance units)
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2006-09-22 00:22:34 +08:00
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>atom_modify map hash
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atom_modify map array sort 10000 2.0
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atom_modify first colloid
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Modify properties of the atom style selected within LAMMPS.
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</P>
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<P>The <I>map</I> keyword determines how atom ID lookup is done for molecular
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problems. Lookups are performed by bond (angle, etc) routines in
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LAMMPS to find the local atom index associated with a global atom ID.
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When the <I>array</I> value is used, each processor stores a lookup table
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of length N, where N is the total # of atoms in the system. This is
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the fastest method for most simulations, but a processor can run out
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of memory to store the table for very large simulations. The <I>hash</I>
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value uses a hash table to perform the lookups. This method can be
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slightly slower than the <I>array</I> method, but its memory cost is
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proportional to N/P on each processor, where P is the total number of
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processors running the simulation.
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</P>
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2008-02-16 03:09:18 +08:00
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<P>The <I>first</I> keyword allows a <A HREF = "group.html">group</A> to be specified whose
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atoms will be maintained as the first atoms in each processor's list
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of owned atoms. This in only useful when the specified group is a
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small fraction of all the atoms, and there are other operations LAMMPS
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is performing that will be sped-up significantly by being able to loop
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over the smaller set of atoms. Otherwise the reordering required by
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this option will be a net slow-down. The <A HREF = "neigh_modify.html">neigh_modify
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include</A> and <A HREF = "communicate.html">communicate group</A>
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commands are two examples of commands that require this setting to
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work efficiently. Several <A HREF = "fix.html">fixes</A>, most notably time
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integration fixes like <A HREF = "fix_nve.html">fix nve</A>, also take advantage of
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this setting if the group they operate on is the group specified by
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this command.
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</P>
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<P>It is OK to use the <I>first</I> keyword with a group that has not yet been
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defined, e.g. to use the atom_modify command at the beginning of your
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input script. LAMMPS will check that the group exists before the
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first simulation is performed.
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</P>
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<P>The <I>sort</I> keyword turns on a spatial sorting or reordering of atoms
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within each processor's sub-domain every <I>Nfreq</I> timesteps. This can
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improve cache performance and thus speed=up a LAMMPS simulation, as
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discussed in a paper by <A HREF = "#Meloni">(Meloni)</A>. In tests we have done,
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the amount of speed-up can range from zero to 3-4x. It is typically
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more effective at speeding up simulations of liquids as opposed to
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solids.
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</P>
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<P>Reordering is peformed every <I>Nfreq</I> timesteps during a dynamics run
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or iterations during a minimization. More precisely, reordering
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occurs at the first reneighboring that occurs after the target
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timestep. The reordering is performed locally by each processor,
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using bins of the specified <I>binsize</I>. If <I>binsize</I> is set to 0.0,
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then a binsize equal to half the <A HREF = "neighbor.html">neighbor</A> cutoff
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distance (force cutoff plus skin distance) is used, which is a
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reasonable value. After the atoms have been binned, they are
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reordered so that atoms in the same bin are adjacent to each other in
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the processor's 1d list of atoms.
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</P>
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<P>The goal of this procedure is for atoms be near each other in the
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processor's 1d list of atoms that are also near to each other
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spatially. This can improve cache performance when pairwise
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intereractions and neighbor lists are computed. Note that if bins are
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too small, there will be few atoms/bin. Likewise if bins are too
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large, there will be many atoms/bin. In both cases, the goal of cache
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locality can be undermined.
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</P>
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<P>IMPORTANT NOTE: Running a simulation with sorting on versus off should
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not change the simulation results in a statistical sense. However,
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reordering will induce round-off differences, which will lead to
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diverging trajectories when comparing two simluations. Various
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commands, particularly those which use random numbers (e.g. <A HREF = "velocity.html">velocity
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create</A>, and <A HREF = "fix_langevin.html">fix langevin</A>), may
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generate different results (but statistically identical) depending on
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the order in which they process atoms. The order of atoms in a
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<A HREF = "dump.html">dump</A> file will also change if sorting is enabled.
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B>
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</P>
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2010-01-14 04:56:56 +08:00
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<P>The map keyword can only be used before the simulation box is defined
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by a <A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A>
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command.
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</P>
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2010-01-14 04:57:58 +08:00
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<P>The <I>first</I> and <I>sort</I> options cannot be used together. Since sorting
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is on by default, it will be turned off if the <I>first</I> keyword is
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used.
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2006-09-22 00:22:34 +08:00
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B>
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</P>
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<P>By default, atomic (non-molecular) problems do not allocate maps. For
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molecular problems, the option default is map = array. By default, a
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"first" group is not defined. By default, sorting is enabled with a
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frequency of 1000 and a binsize of 0.0, which means the neighbor
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cutoff will be used to set the bin size.
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</P>
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<HR>
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<A NAME = "Meloni"></A>
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<P><B>(Meloni)</B> Meloni and Rasati, J Chem Phys, 126, 121102 (2007).
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</P>
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</HTML>
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